seq=getSequence(id=c('7407','7264'), type='entrezgene', seqType ='coding_gene_flank', upstream = 200, mart = ensembl)
it raises the error,
Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"), :
Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT FOUND
But sometimes it just works and return the 100bp upstream promoter sequences.
Don't know why does this error come out casually.
Also, when I retrieve the 100bp upstream promoter sequences of entrez gene 7407 and 7264, it returns more than 1 sequences.
coding_gene_flank entrezgene
533 CCTCTGAGAGCCAGGTCCTCGGCTCCTGACAGCCTGCCTGGTCAGA... 7407
587 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN... 7407
12137 TGTAGGCTGAGAGCTCCCAGGGGAACAGGGCTGCGACGAGGGAGTG... 7264
12271 CTCCCCTAAGGGCTGGCCCTGGGGCCCTGCCGGGGGAGCCGGAGCA... 7264
why dose it return more than 1 sequence for each entrez id? and why is one of the sequences of 7407 all 'N's?
Appreciate that if you can answer my question!
Thanks in advance!
Best regards,
Ray